A replica of Christopher Columbus' flagship, the Santa Maria, makes its way past the Portuguese island of Madeira on Sept. 12, 2011. / Eric Risberg, AP

by Traci Watson, Special for USA TODAY

by Traci Watson, Special for USA TODAY

What might be one of the world's greatest archaeological treasures nearly slipped through Barry Clifford's grasp.

Back in 2003, Clifford, an underwater archaeological explorer, and his crew discovered a tantalizing shipwreck off the coast of Haiti. The wreck sat in exactly the spot where Clifford reckoned Christopher Columbus' flagship, the Santa Maria, had sunk on Christmas Day in 1492, less than three months after Columbus reached the New World for the first time.

Archaeologists "eliminated the site as not being what we were looking for," Clifford told USA TODAY in an interview Tuesday. He went on to make an exhaustive survey of the waters off Haiti, "spending a small fortune â?¦ (and) eliminating every other possibility, to the point where I threw my hands up in the air, and I don't do that very often."

Today, a few weeks after returning to the wreck, Clifford, who discovered the pirate ship Whydah, says he thinks there's strong evidence his team has indeed snagged one of the most sought after archaeological sites in the history of human exploration. He says the once-scorned shipwreck is the Santa Maria, the slow, tubby but solidly built rental vessel that carried Columbus and his men on the voyage that revealed the existence of the New World to the Old.

The team's return to what could be the bones of the Santa Maria sprang out of a late-night revelation about nine years after the team located the wreck. Clifford, who'd been studying 15th-century ordnance, bolted awake to the realization that a tube his son had photographed in the wreck in 2003 was a lombard, an open-ended cannon popular during Columbus' day. That led to the realization that he'd probably found the Santa Maria, only to abandon it.

He and his team returned to the site a few weeks ago, only to find it looted of the lombard, several wheels that would've been used to maneuver the cannon and a piece of the rudder mechanism. Other evidence from the site strongly points to the wreck being the Santa Maria, he said.

Columbus wrote that the wreck was 1Â½ leagues from La Navidad, the fortified encampment he founded in what is now Haiti after the loss of the Santa Maria, Clifford said. The wreck sits the equivalent of 1Â½ leagues from the site suspected to be La Navidad.

The wreck's resting place lies near breaking waves, as Columbus reported. It was in a sandy spot, as implied in Columbus' journal.

At the site, the team found a field of stones 40 feet long and 20 feet wide. That corresponds to the likely dimensions of the Santa Maria, which would've carried ballast stones in her hold.

"Everything fit the equation," said Clifford, who added that the team ruled out other wrecks in the same vicinity. He has a Haitian permit to explore the wreck but doesn't plan to proceed immediately. The top priority, he said, must be the protection of the wreck from looters.

Clifford suspects treasure hunters nabbed the most accessible artifacts, including the lombard. He has only a photograph of it, and he hopes a benefactor will step in to offer a reward for information on the whereabouts of the artifacts.

There may be much more to find. There could be wooden remnants of the ship buried in the sediments, Clifford said, and more.

"It's a big pile of rocks," he said, "but there's a lot more to it than that. I'm not going to tell you what it is."

One outside expert says Clifford may be onto something.

"There is some very compelling evidence from the 2003 photographs of the site and from the recent reconnaissance dives that this wreck may well be the Santa Maria," Indiana University's Charles Beeker told The Independent, the British newspaper that first reported the discovery.

Another expert expresses caution.

"If this is a very early Spanish shipwreck, it should be looked at by a number of different people who are experienced in â?¦ archaeological sites from that time period," said Roger Smith, Florida's state underwater archaeologist, who has long experience studying shipwrecks.

To be sure the ship is the right vintage, experts would have to examine the design of the hull, evidence for how the ship was rigged, the placement of its arms and how it was built, Smith said. When an early shipwreck was discovered off Pensacola, Smith and his colleagues brought in experts on coins, old wood, stones and plant and animal remains to help identify the vessel.

"It's easy to jump to conclusions when people keep asking, 'Is this Columbus's ship?' " Smith says. "The ship will tell its own story."